Accuracy in tRNA splicing is essential for the formation of functional tRNAs and, hence for gene expression. In Bacteria, tRNA introns are self-splicing group I introns and the splicing mechanism is autocatalytic. In Eukarya, tRNA introns are small and invariably interrupt the anticodon loop one base 3′ to the anticodon. In Archaea, the introns are also small and often reside in the same location as eukaryal tRNA introns.
In both Eukaryotes and Archaea, the specificity for recognition of the pre-tRNA resides in the endonucleases. These enzymes remove the intron by making two independent endonucleotytic cleavages. The archaeal enzyme acts without any reference to the mature domain (mature-domain independent mode, MDI) but instead recognizes a structure, the bulge-helix-bulge (BHB) motif, that defines the intron-exon boundaries. The eukaryal enzyme normally acts in a mature-domain dependent mode (MDD); the enzyme recognizes a tripartite set of RNA elements. One subset of recognition elements is localized in the mature domain, while two other subsets are localized at the exon-intron boundaries. A pivotal role is played by a base-pair located near the site of 3′ cleavage, the so-called anticodon-intron pair (A-I pair). A purine is strongly preferred at the position preceding the 5′ cleavage site.
The primary and secondary structures at the exon-intron junctions of the archaeal and eukaryal pre-tRNAs do not show evident similarities, with the exception of the three-nucleotide bulged structure, closed by the A-I pair and containing the 3′ cleavage site, that resembles half of the BHB. The endonuclease are evolutionarily related, but their substrate recognition properties appear drastically different. It has previously been shown, however, that the Xenopus and the yeast endonucleases retain the ability to operate in the MDI mode.